To reproduce:
1) Open the attached project and scene
2) Note down how it looks (right view in the screenshot)
3) Open Lighting Window
4) Generate Lighting (or enable Auto Generate and let it bake)
5) Notice that the scene is fully lit now (left view in the screenshot)
6) Clear baked data (if you enabled Auto Generate, have to disable it first)

Expected: The scene should look the same as in step 2
Actual: Only parts of baking are cleared from the scene/game view (middle view in the screenshot)
Workaround / Note: If you play the scene or restart the Editor, Scene/Game View starts showing the correct output. Screenshot of all three states in the edit below

Reproduced in 2017.4.0f1, 2020.1.0a15